Unfortunately, the window control buttons (red, yellow, green) overlap standard navigationItem.leftBarButtonItems defined in a UIViewController subclass. I don't think we're all supposed to somehow fix that in our apps? How would we?

Here's the link to that documentation screenshotted above: https://developer.apple.com/documentation/bundleresources/privacy_manifest_files/describing_data_use_in_privacy_manifests

Is there any timeframe on when this bug will be fixed? It is affecting all iOS 16 users.

This fixed it for me too. Updating macOS, and it also updated Safari with that to 14.1.2 and problem seems to be gone so far.

This should not be an accepted answer. The issue still persists as of Safari 14.1.1, macOS 11.4.